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Jin-Dong Kim
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NameDescriptionUpdated at
11-12 / 12 show all
CORD-19CORD-19 (COVID-19 Open Research Dataset) is a free, open resource for the global research community provided by the Allen Institute for AI: https://pages.semanticscholar.org/coronavirus-research. As of 2020-03-20, it contains over 29,000 full text articles. This CORD-19 collection at PubAnnotation is prepared for the purpose of collecting annotations to the texts, so that they can be easily accessed and utilized. If you want to contribute with your annotation, take the documents in the CORD-19_All_docs project, produce your annotation to the texts using your annotation system, and contribute the annotation back to PubAnnotation (HowTo). All the contributed annotations will become publicly available. Please note that, during uploading your annotation data, you do not need to be worried about slight changes in the text: PubAnnotation will automatically catch them and adjust the positions appropriately. Once you have uploaded your annotation, please notify it to admin@pubannotation.org admin@pubannotation.org, so that it can be included in this collection, which will make your annotation much easily findable. Note that as the CORD-19 dataset grows, the documents in this collection also will be updated. IMPORTANT: CORD-19 License agreement requires that the dataset must be used for text and data mining only.2020-04-14
Glycosmos6This collection contains annotation projects which target all the PubMed abstracts (at the time of January 14, 2022) from the 6 glycobiology-related journals: Glycobiology Glycoconjugate journal The Journal of biological chemistry Journal of proteome research Journal of proteomics Carbohydrate research 2023-11-16
Projects
NameTDescription# Ann. Updated atStatus
101-110 / 160 show all
Grays_part2_test8.57 K2023-11-29Testing
LitCoin-GeneOrGeneProduct-v2threshold = 0.938.98 K2023-11-29
metamap-sampleSample annotation of MetaMep, produced by Aronson, et al. An overview of MetaMap: historical perspective and recent advances, JAMIA 201010.9 K2023-11-27Testing
semrep-sampleSample annotation of SemRep, produced by Rindflesch, et al. Rindflesch, T.C. and Fiszman, M. (2003). The interaction of domain knowledge and linguistic structure in natural language processing: interpreting hypernymic propositions in biomedical text. Journal of Biomedical Informatics, 36(6):462-477.11.1 K2023-11-29Testing
CORD-19-SciBite-sentences11.2 K2023-11-26Testing
uniprot-mouseProtein annotation based on UniProt11.5 K2023-11-28Developing
EDAM-topicsannotation for EDAM topics11.6 K2023-11-29Testing
EDAM-DFOannotation for EDAM terms for data, formats, and operations12.5 K2023-11-29Testing
LitCovid-sample-Enju13.1 K2023-11-29Developing
LitCovid-PD-MONDO-v1PubDictionaries annotation for disease terms - updated at 2020-04-20 It is based on MONDO Version 2020-04-20. The terms in MONDO are loaded in PubDictionaries, with which the annotations in this project are produced. The parameter configuration used for this project is here. Note that it is an automatically generated dictionary-based annotation. It will be updated periodically, as the documents are increased, and the dictionary is improved.13.4 K2023-11-29Released
Automatic annotators
NameDescription
21-30 / 39 show all
PD-NCBITaxon-B
PubTatorPubTator annotation provided by NCBI
PD-CHEBI-B
PD-GlycoGenes20190927-B
PD-GO-BP-BBiological Processes as defined in GO
PD-HP-B
PD-HP
PD-CLO-B
PD-HP-PA-B
PD-HP-PA
Editors
NameDescription
1-2 / 2
TextAE-oldTextAE version 4, which was the latest stable version until Apr. 19, 2020.
TextAETextAE version 5, which enables edition of attributes of denotations.